.. baredSC documentation master file, created by
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Welcome to baredSC's documentation!
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BARED (Bayesian Approach to Retreive Expression Distribution of) Single Cell
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baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. It uses the raw counts and the total number of UMI for each cell. The PDF is approximated by a number of 1d or 2d gaussians provided by the user. The likelihood is estimated using the asumption that the raw counts follow a Poisson distribution of parameter equal to the proportion of mRNA for the gene in the cell multiplied by the total number of UMI identified in this cell.

.. toctree::
   :maxdepth: 2
   :caption: Contents:

   content/installation.rst
   content/usage.rst
   content/outputs.rst
   content/tutorial_sim.rst
   content/releases.rst

Indices and tables
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* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`